The inner part of Isahaya Bay was converted to a freshwater reservoir following the closure of the land claim dike in 1997. Turbid water drains into Isahaya Bay when water levels increase. We investigated whether particulate organic matter (POM) from the reservoir in Isahaya Bay has caused bottom organic enrichment in the northern part of Ariake Bay. Using potential end-members from before to after the rainy seasons, during which a frequent discharge from the reservoir was expected, stable isotope analyses were performed on sediments collected from Isahaya Bay and northern Ariake Bay. Each end-member was isotopically differentiated by δ13C and δ15N (riverine POM: −28.5 to −27.2‰ and 3.3–4.6‰; reservoir POM: −25.7 to −25.3‰ and 7.4–8.4‰; marine POM: −21.8 to −19.7‰ and 6.7–7.6‰; microphytobenthos estimated from consumers: −16.1 to −15.9‰ and 5.2–6.1‰, respectively). Sediment isotopic signatures fell within the mixing space defined by the signatures of the end-members. Marine POM contributed greatly to bottom sediments in both seasons in Isahaya Bay and Ariake Bay, ranging from ca. 60–70 and 40–60%, respectively. Reservoir POM contributed around 10% to bottom sediments. This percentage slightly increased in the sediment of Isahaya Bay after the rainy season, but decreased in the sediment of Ariake Bay. Thus, most of the POM discharged from the reservoir would not reach the northern part of Ariake Bay and would not be a major contributor to organic enrichment. This study is the first to quantitatively describe the contribution of drained reservoir POM outside Isahaya Bay.